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1 #!/bin/bash
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2
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3 #sample_data=(tmp tmp1 tmp2 tmp3)
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4 sample_data=(`cat $1 | cut -f1 | sed ':a;N;$!ba;s/\n/ /g'`)
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5 #sample_name=(sample1 sample2 sample3 sample4)
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6 sample_name=(`cat $1 | cut -f2 | sed ':a;N;$!ba;s/\n/ /g'`)
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7 #sample_group=(gr1 gr1 gr2 gr2)
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8 sample_group=(`cat $1 | cut -f3 | sed ':a;N;$!ba;s/\n/ /g'`)
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9
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10
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11 group=('#')
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12 sample=('#Feature')
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13
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14 touch anno.tmp
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15 touch count.tmp
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16
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17 nsamples=`expr ${#sample_data[@]} - 1`
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18
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19 for i in `seq 0 1 $nsamples`; do
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20 group+=(${sample_group[i]}:${sample_group[i]})
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21 sample+=(${sample_name[i]})
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22
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23 cat ${sample_data[i]} | tail -n+3 > dataWithoutHeader 2>> script.log
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24
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25 cat dataWithoutHeader | sort -k1 > dataWithoutHeader.sorted 2>> script.log
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26
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27 cat dataWithoutHeader.sorted | awk '{print $1}' > anno.sample 2>> script.log
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28 cat dataWithoutHeader.sorted | awk '{print $5}' > count.sample 2>> script.log
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29
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30 paste -d"\t" count.tmp count.sample > count 2>> script.log
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31 paste -d"\t" anno.tmp anno.sample > anno 2>> script.log
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32
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33 cat count > count.tmp 2>> script.log
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34 cat anno > anno.tmp 2>> script.log
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35
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36 done
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37
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38 echo ${group[*]} | sed -e 's/ /\t/g' > count.matrix 2>> script.log
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39 echo ${sample[*]} | sed -e 's/ /\t/g' >> count.matrix 2>> script.log
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40
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41 cat count | cut -f 2- > count.tmp 2>> script.log
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42
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43 paste -d"\t" anno.sample count.tmp >> count.matrix 2>> script.log
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44
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45 cat anno.tmp | cut -f 2- | awk '{for (i=2; i<=NF; i++){if ($1!=$i){print "error"; break}}}' > control.data 2>> script.log
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46
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47 echo -e "gene_ID\tstart_coord\tend_coord" > annotation 2>> script.log
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48 cat dataWithoutHeader.sorted | awk '{print $1"\t"$2"\t"$3}' >> annotation 2>> script.log
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49
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50 if [[ -s control.data ]]; then
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51 echo "kolumny nie sa w odpowiedniej kolejnosci" > error.log
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52 echo "" > count.matrix
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53 echo "" > annotation
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54 else
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55 echo "" > error.log
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56 fi
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